The Avengers: Out of Time
by Katterina
Summary: A little idea that popped into my head. What happens when the 12th Doctor is a girl, and she meets the Avengers. The TARDIS is ruined, and now she needs the help of Earth's Mightiest Heroes. Adventure and some romance. 12thDoctor x Ironman.
1. Prologue: Priority 9

**Prologue:**

"Priority 9, sir," the young agent reported to Director Fury rather timidly.

"Priority 9?" Fury asked with eyebrow raised. "Has Torchwood confirmed this?"

Another agent came forward to answer that question. "Torchwood confirms that the energy signature is indeed the T.A.R.D.I.S." she spoke with a hand to her earpiece, relaying information as it was received. "Only problem is sir, the T.A.R.D.I.S appears to be crashing…"

* * *

The Doctor did all he could but it wasn't enough. The TARDIS was crashing through time and space. Her heart and soul had been damaged beyond repair. There was only one thing he could do to save her. He turned to River, who had been desperately trying to slow their fall.

In one quick movement he pulled River into his arms and kissed her firmly. After the kiss he whispered, "Goodbye River." Then he finished reprogramming her vortex manipulator for its final, one way, trip to safety. She gave him a panicked wide eyed look before she vanished.

He took a moment to pause in the sadness, and then he got down to business. He opened the heart of the TARDIS and let the remainder of her soul into his mind.

"Goodbye River. Goodbye Ponds. Goodbye…" he breathed out as all the pain of regeneration took him.


	2. Chapter 1: The Crash

**Chapter 1:**

"We have a Priority 9," Nick Fury said to the assembled Avengers.

"What is a Priority 9?" Thor asked with a mild confusion to his tone.

"Priority 9," Nick Fury began. "Is The Doctor. Priority 9 means The Doctor has returned."

Thor jerked his head up at the name in recognition.

"We need someone to go and find The Doctor for us and bring him back here." Fury explained to the group. He looked around at the assembled faces as the screen behind him showed various information on the Doctor.

Thor looked nervous. Natasha looked bewildered as did Hawkeye. Bruce looked stunned. And Tony, well he just looked more interested than normal. Of course that was probably because of the pure scientific possibilities that The Doctor represented.

"Thor, you seem to recognize The Doctor, how about you go?" Fury suggested as he surveyed the group. This caused Thor to almost jump in surprise. His expression when he turned to look at Fury was as close to panic as Fury had ever seen cross the Asgardian's face.

"With respect Nick Fury, I would have to decline. Our people hold a wary respect for The Doctor, and as a result we have stayed far out of his way," Thor spoke carefully. His people had met the Doctor in the past, and they knew he was a Time Lord, the last actually. And he was to be respected, and feared!

Fury nodded in reply. He wasn't surprised that the Asgardians knew about the Doctor. He suspected that all alien races knew The Doctor.

"Who then? Who should go to collect the Doctor? After this whole mess with Loki we need the Doctor more than ever to help us prepare for any future invasions. Plus the Doctor would be the perfect person to help us deal with the aftermath of Loki's visit." Fury spoke as he walked around the table behind each member.

"I'd go, but I'm not sure the other guy wouldn't get provoked," Bruce said with a faint smile.

"Which is just as well," Fury said, his tone held a hint of a laugh. "I'd hate to see what happened if you and certain members of Torchwood met."

"I'll go," Tony interjected then. "I'm interested in seeing this T.A.R.D.I.S. I don't think I have anything to worry about meeting some members of this Torchwood."

Fury pursed his lips together in disapproval, but no one else volunteered. Even when he looked at Black Widow and Hawkeye, who carefully avoided his eyes. Captain America looked too overwhelmed to be useful in this circumstance.

With a deep and tired sigh Fury gave a single nod to Tony Stark. "Very well, doesn't seem like there's much choice. I leave the recruitment of the Doctor to you…"

"God help us all…" Captain America muttered from his stunned silence.

Tony arrived at the crash site that night, just as Torchwood as was pulling up. He landed next to the SUV and looked at the mess of the area around him. As a man emerged from the SUV Tony opened the face plate to his suit. The man was tall with dark hair and blue eyes. He was wearing a old military coat. He looked from the mess around them to Tony.

"Captain Jack Harkness, and you must be Iron Man…" Jack introduced himself with a halfhearted grin. He noticed that Tony Stark was quite good looking, but all of his attention was on finding the Doctor in this chaos.

The forest around them was destroyed. The trees in splinters all over the place. It looked like they were at ground zero for some type of explosion. There were pieces of machinery and blue painted wood spread over an area of 30 feet in all directions. And at the center was a crater was a glowing ball of golden energy.

"Oh Doctor…" Jack breathed with pain in his voice. He rushed forward to the ball of glowing energy, jumping over debris of trees and machinery alike. Tony followed close on his heels.

When they reached the edge of the crater, they looked down into the glowing ball to see a woman. A naked woman curled up in a ball and barely breathing. She was pale with a short mess of ginger hair on her head. And she appeared to be sleeping.

"A woman…?" Tony said in surprise. As they both looked down at her.

"A woman indeed," Jack said with a stunned tone.

"Well, we need her help if she's the Doctor," Tony said as he moved towards her.

"No!" Jack shouted as he moved in front of Tony with his arms out. "You can't take her, she's still regenerating! She might not know who and where she is when she wakes."

"And she'd be better off here, in the middle of the woods, with you?" Tony asked as he lowered the faceplate. "We need her, and we're taking her." His voice came out with its metallic tint now that he was fully suited again.

Jack pulled a gun on Iron Man as he lowered his face plate. "No! She's not going anywhere with you and your SHIELD goons."

"I wouldn't do that Captain Harkness," Tony said as he trained his weapons systems on the man. "Mine are bigger."

Jack assessed the multitude of weapons trained on him, and lowered his pistol. "Fine, but I'm going with you!" He wasn't going to give up here. He was going where the Doctor went.

"Fine," Tony said as he moved past Jack to pick up the beautiful naked ginger woman. "But I don't think Fury is going to like having you tag along."

"Well that's his problem now," Jack said with a smile. "Isn't it?"


	3. Chapter 2: A New Face

**Chapter 2:**

Several hours later aboard the S.H.I.E.L.D. ship The Doctor opened her eyes slowly. "Well…" she started to say then covered her mouth with a hand in surprise. Her dark blue eyes widened. "I'm a girl?" she exclaimed behind her hand, though it came out sounding more like, "Mm ahh grrrlll?"

She stopped covering her mouth to feel at her hair. "Short hair," she mused as she pulled a strand down where she could see it. "And finally GINGER!" She noticed that her accent was slightly Irish when she spoke.

"Okay," The Doctor said as she evaluated herself. "Ginger, Irish, and…" She looked down, "defiantly female!" She took in her creamy pale skin, covered with freckles, and very busty nakedness. Slim, but curvy, the Doctor noticed.

She finally stopped wondering over her newest form and took in her surroundings. She was in a metal room with a small bunk, which she was currently sitting on. There was a small desk and a chair and only one door in and out of the room. There was thankfully a robe sitting on the chair. It was a simple cotton robe of blue color.

The Doctor slipped on the robe and then spotted the camera in the corner above the door.

"Hallo, there!" She called up to the camera. "Might I come out and meet those responsible for bringing me here after my fall?" At that the door opened on its own.

She ventured out into the narrow metal corridor. "Defiantly on a ship…" she muttered as she followed the corridor. "Looks like a military ship. American. 21st Century. And…" she paused, feeling the thrum of the engines through her feet. "Flying! How extraordinary!"

"That is correct Doctor," Fury said as he rounded the corner at the end of the corridor. "Welcome to SHIELD central command." Fury said as he lifted his hands to incase the ship. Then he motioned for the Doctor to follow him.

The Doctor rounded the corner behind Fury and came onto the bridge of the SHIELD ship. There were many people running around from console to console. And there was a group of people seated at a table nearby. And boy, were they interesting people.

One of them was from Asgard. "Lovely place Asgard, haven't been there in a millennia," the Doctor mused as she looked at Thor. She remembered him from a previous visit with Odin, though he had been just a boy at the time. "Thor Odinson. You've grown quite a bit!" she exclaimed as she looked at his huge muscles. "Quite a big, bigger," she added vaguely.

"Doctor," Thor nodded in respect keeping his eyes down. "You've changed mightily."

"Oh, well I suppose I have since you last saw me…" The Doctor said absently. "Several times."

"And who else do we have here?" She spoke as she walked around the table. "A scientist with certain calm issues…" she said with a smile at Bruce Banner. "Lots of information about you in the future!" Bruce blushed and smiled back.

"The man out of time," She said to Captain America. "I know they call you that, but it might help you to know that you are exactly where you are supposed to be." Steve looked surprised at that, but perhaps a bit more relaxed.

"A spy and her boyfriend," The Doctor continued as she passed Black Widow and Hawkeye. Both of them tried to protest the last bit, but she wasn't listening to them anymore.

"The master spy of all spies," she said with a nod to Nick Fury. "Nice eye patch."

"And last of all: a billionaire with a fancy for mechanical suits," She said as she sat next to Tony Stark in the only empty seat. She started to put her feet up on the table, but quickly realized that she would end up showing off her new lady bits to the room if she did that. Instead she crossed her legs all lady-like, as she had seen Amy do many a time in her short skirts.

"So why am I sitting with the group known as the Avengers, on a flying battleship owned by the Strategic Hazard Intervention Espionage Logistics Directorate? Quite a mouthful that," The Doctor questioned the group sitting around her. "And why do I have no clothes?" She added as an afterthought.

Fury stood up again and pushed a button to turn on the screen behind him. "Yesterday," Fury said as the images from the crash site filled the screen. "Your TARDIS exploded upon crash landing in the forests of the Oregon." Fury watched closely as the Doctor's face showed brief signs of pain. "We sent Mr. Stark here to rescue you," Fury said with a nod to Tony, who was currently toying with a clear data file.

"We need your help Doctor," Fury said as the screen changed to show the aftermath of the Chitauri attack. "We've needed your help for some time now."

"How did the Chitauri get all the way out here?" The Doctor asked with a tilt of her head. "They don't possess the technology at this point in time to get to Earth."

"They had a little help," Fury started.

"From Loki," Thor added a bit sullenly.

"Your brother, I remember him. A bit of a cruel sense of humor on that one." The Doctor spoke.

"Yes, well… he's adopted," Thor replied a bit glum.

"Ah, so you finally learned he was one of the frost giants, that's good. But he's not a Chitauri, and he couldn't have done this alone." The Doctor said quite sure of her statement.

"And a device called the Tesseract," Fury finished.

The Doctor sat up straighter at that. "The Tesseract? Where is the tesseract now?" Her voice was filled with alarm.

"Safe, on Asgard." Thor replied with a firm tone.

"Ah… I see. Well I guess that's as good a place for it as any for now…" The Doctor replied a bit absently as she seemed to think about things. "So why no clothes? You never answered that."

"We found you like that," Tony said with a grin.

"Oh, you did?" She replied for a moment. Then she seemed to realize what he had said and she turned a nice shade of pink. "Oh… you did. Well, and with me being of the female type now, I guess that would be… quite improper of you!" She turned and slapped Tony in the face lightly.

"Hey!" He said in shock. "It's not like I fondled anything improper…much."

"Well, okay then," The Doctor said with a light smile. "If that's all." Then she seemed to think about it and frowned.

"I have some clothing that might fit you," Natasha said with a quick glance at the Doctor's frame. "Though they might be a bit tight around the chest area."

The Doctor looked down at her chest and then glanced over Natasha's chest. "I suppose that would be true. Well then, let's get to it so I stop hanging about in a dressing gown." She stood up and looked expectantly at Natasha.

Natasha looked at Fury who nodded before she stood up led the Doctor to her quarters. When they got there she tossed a few things from her closet to the Doctor. "Here you go. There's a few choices there for you." Then she turned her back to the woman who was now naked in front of her. The bathrobe was discarded and the Doctor was sorting through the clothing.

She eventually settled on a nice pair of jeans, a nice burgundy blouse, a blue scarf and a wool coat in added a pair of comfortable riding boots and checked out her appearance in the mirror. "That'll do."

Now, fully dressed, she turned around to find Natasha had gone back to the briefing area. So she followed the corridor back to the deck and announced to the assembled group with a flourish, "I will help out with your little problem, but I require help with my ship." She looked pointedly at Stark as she finished her statement.

"And I'm going to help you both," said a voice from behind the Doctor. She turned to find the smiling face of Captain Jack Harkness beaming at her.

"It's good to see you Doctor!" Jack added as he moved to hug the woman who was once HIS Doctor.

"Good to see you too Jack," The Doctor squeaked out as he hugged her tightly.


	4. Chapter 3: Pieces of Time

**Chapter 3:**

Later that day they were standing in the middle of nowhere in the Oregon coast forests. The location was the site of the TARDIS crash. "They" included The Doctor, Captain Harkness, Tony Stark, Bruce Banner, and a few stragglers from both SHIELD and Torchwood.

The Doctor looked around her and felt the beginnings of tears stinging her eyes. "Oh my dear beautiful TARDIS, look at you…"

Jack stepped up to the Doctor and placed a hand on her shoulder. "I'm so sorry," he said as he gazed around at the remains with her. He wanted to hold her, but he didn't think she'd let him. So he just stayed by her, lightly touching her shoulder.

Tony watched them closely for a moment, then he moved through the wreckage looking at various parts of technology that was so far beyond him that it was completely captivating. As he scanned parts with his tablet he thought about the Doctor. She and Captain Harkness definitely had a history, but her reactions towards Harkness showed that she wasn't as interested in him as he was in her.

That was good for Tony because he was certainly interested in the Doctor. How could he not be? The Doctor seemed to have a way of fascinating those around her. Plus this incarnation of her, if he actually believed that bit, was a smoking hot redhead and Tony was starting to feel lonely since Pepper left him a few months ago.

The Doctor looked around her sadly, but she started doing an inventory in her head of the parts that she could see that could be repaired and the parts she would have to rebuild. She shrugged off Jack's hand as she moved up next to Tony Stark. He was scanning bits of the TARDIS with some sort of clear hand held computer.

"Do you know what it'll take to rebuild this?" Tony asked her once he noticed her. "Because this technology is so far beyond anything I've ever seen."

"There are things in your time that can be… modified," The Doctor answered him with a sad smile. "Things that you might just be able to help me figure out. You're a brilliant human Mr. Stark. I don't think I can pull this off without your help." She patted his arm awkwardly and turned to go examine a piece of wood.

Bruce came up behind Tony and was shaking his head. "If the file can be believed, I don't think you're quite her type Tony."

"Nonsense, I am every woman's type," Tony jested with a half hearted grin. "It's just that she's not used to being a woman yet, that's all."

"If you say so," Bruce shrugged as he watched the Doctor pick up the piece of wood with charred edges. The piece had writing on it, but he couldn't make it out from where he was standing. Something like "public call…"

"She seems so sad," Bruce said as Jack Harkness came up to them.

"That's because she is," Jack said when he came up between them. "She's just lost her oldest friend."

"What? The spaceship?" Bruce asked confused.

"Yes, the spaceship!" Jack snapped back then he gave a little shake of this head and tried to figure out how to explain. "The TARDIS is more than a spaceship or a time machine. The TARDIS is, or was, alive. The Doctor's oldest friend and companion."

"So this, all this was a living thing?" Bruce said with a wave of his hands around at the mess they were standing in.

"Jack!" The Doctor called from off to the left near the edge of the destruction, cutting the conversation short. "Look what I found!"

Jack turned to her at the sound of her yelling and a very familiar noise of the sonic screwdriver. The Doctor was waving her sonic screwdriver around above her head in triumph. "Well that'll help!" Jack yelled back at her with a big grin on his face.

Tony scanned the energy signature that was coming off of the item the Doctor was holding. It seemed to be some form of sonic technology that changed its purpose depending on the setting. He was instantly fascinated and a bit jealous.

"Can I see that?" He asked the Doctor as she came up with them with her prize in hand. She eyed him appraisingly for a moment then handed the "screwdriver" over. "I'll need that back in a moment." She said with a wink.

"Okay…" Tony said a bit absently as he started trying to figure it out. He found himself walking behind her while he fiddled.

"Geronimo!" The Doctor exclaimed as she came across a larger piece of machinery with a circle on it that almost looked like a form of language. "_This_ we can work with!"

She grabbed the piece and cradled it like a baby. "Oh my dear, dear sexy box, we'll get you back to normal soon enough," she whispered to the machinery. She held her hand out to Tony and requested, "Screwdriver." Then she pointed the sonic screwdriver at the piece of machinery. There was a small spark and a light came on for just a moment, but it was enough to lighten her mood and give her hope.

"Alright everyone I need you to gather every piece you can of machinery and anything blue." She ordered the people around her suddenly.

Then she turned her attention to Stark. "I need a place to work on all this."

"I worked out just the place before we left the ship," Tony said with a sly wink. "So would you like me to take you to your new workshop, Doctor?"

"Oh yes," the Doctor whispered with smile. "Please!"


	5. Chapter 4: Lost Bits

**Chapter 4:**

Tony took her to the car and then drove them to the warehouse in Portland with an apartment above it. On the hour long drive the Doctor couldn't help but lament about how slow everything seemed to move for humans. "Is it always this slow to get around?"

"Well, I'm used to a faster vehicle than your Torchwood friends provided," Tony suggested but he knew it wasn't what she was referring to.

"What's it like?" He asked her after a moment silence passed.

"What, time travel?" She asked him with a raised eyebrow. "It's the most fantastic thing ever you'll ever know. And the loneliest." The last comment was barely even a whisper.

Tony drove the rest of the way in silence, he was thinking about what she had said. Then they arrived, as the evening was falling. The darkening sky started to show hints of stars. The breeze held a scent of approaching summer to it.

He stopped the SUV and they got out. The Doctor looked around them with interest. They were in a suburb of the city and there were few lights on. The land surrounding the warehouse was all farmland and other warehouses. They were a ways away from any houses. The perfect setting to rebuild a TARDIS.

"Does this belong to SHIELD?" the Doctor asked Tony as he moved to unlock the small side door.

"No," Tony answered. "It belongs to Stark Industries. I find it useful to have warehouses all over the country, just in case."

As he unlocked the door the lights came on and the Doctor could see a large, but very modern and tech filled room with a staircase in the corner. Then a voice came out of the walls. "Good to see you sir," said the slightly British voice.

"Good to see you too Jarvis," Tony answered the voice with a smile. "We have a guest. Jarvis I'd like you to meet The Doctor."

"Always a pleasure to meet a famous historical figure," the voice of Jarvis said politely.

"An artificial intelligence?" The Doctor asked with the wide eyes of an excited child. "How brilliant!"

"Thank you," Tony said with pride. "I created him many years ago."

The Doctor didn't even acknowledge Tony as she walked up to a control panel in the wall. She ran her sonic screwdriver over the panel for a moment then examined the screwdriver. "How utterly brilliant, and connected to all your properties, as well as running your suits! So what do you think about your creator Jarvis?" She asked the panel.

"Oh, I put up with him." Jarvis said with a hint of weariness to his voice. "He can be a real challenge sometimes."

"Jarvis," Tony warned.

"Well, she did ask, sir." Jarvis answered, completely unrepentant.

"An artificial intelligence with a very distinct personality," she said as she clapped her hands together once, happily. "You, sir, are amazing!"

"Thank you," both Tony and Jarvis said at the same moment.

"Oh I suppose you are too Mr. Stark…" the Doctor replied back absently as she beamed at Jarvis's console.

It was about that moment when they heard a vehicle pull up to the warehouse.

"Sir, the first Torchwood vehicle has arrived with its load," Jarvis informed Tony. "Should I open the bay doors?"

"Yes, Jarvis," Tony replied as he walked to a far wall and fiddled with a panel on it.

"Thank you," The Doctor added for him to the A.I.

"You are most welcome, Doctor." Jarvis replied, sounding pleased.

The first vehicle to arrive held Bruce Banner, a Torchwood driver, and a couple SHIELD agents that helped unload the precious pieces. It took them a good half an hour to unload that van because the Doctor wanted them to lay out the pieces in just a certain way.

During that time the second van arrived, followed not to long after by a semi truck with the majority of the pieces. Jack arrived with the second van and he tried his best to help the Doctor direct the process.

Eventually Tony Stark walked over to where they were working. He was in one of his mechanical suits.

"I'm going to go make sure they got everything. I'll be back," and with that statement he flew up through the skylight that opened for him to exit.

The Doctor watched him go with a smile on her face. The man was a genius, too bad he had obligations on Earth. She would love to travel with him. With a sigh she turned her attention back to the task at hand.

Tony flew out to the crash site, letting Jarvis put him on autopilot. His thoughts raced around from the incredible tech he had seen to the owner of that tech; The Doctor. He found himself more and more drawn to her, which he could tell was going to be a bit of a problem.

But there was just something about her that he couldn't get out of his head. He wanted to impress her, to help her, and see her smile. It seemed to him like she just had that effect on everyone around her. People wanted to be around the Doctor.

He took the suit off autopilot as he neared the crash site. Then he used the onboard scanners to look for any trace of alien technology as he flew over every square foot of the site. After a few minutes he spotted something in the trees at the edge of the destruction.

It lit up his HUD with residue energy. Carefully he landed near the item and walked over to it in the dark woods. His suit spotlight illuminated the area where the item was lying and he saw it in the light, gleaming silver in the dark. It had a red light that blinked on and off periodically, but not with any regular pattern.

His HUD told him nothing useful about it, other than it was alien, and of a different make than the rest of the pieces he had seen so far. He carefully picked it up and deposited the palm sized ball in one of his compartments.

Then he did one more fly over to check for any more lost parts. His scans showed no more pieces left behind so he started back to the warehouse.


End file.
